The revolution in DNA sequencing technologies during the past decade and ahalf has resulted in an outburst of genome
sequence information for morethan 800 organisms. Genomes of many humans from different ethnic backgroundshave been
sequenced at varying degrees of coverage using multipletechnological platforms and strategies and the effort is ongoing;
thousandsof human genomes will be available in the next few years for researchersto analyze. A major challenge ahead
is to determine the functional componentsof the different genome sequences and how they vary across individuals andspecies.Traditionally
most efforts have focused on the analysis of protein-coding genes.These are typically annotated as exons separated by
introns. Genes are transcribedinto messenger RNA (mRNA), the introns are spliced out, and the exons aretranslated
to protein. In addition we now know there is a plethora of informationin non-coding DNA sequence as to how to regulate
the expression of the genecodingregions. In this chapter we cover the major categories of genomic sequenceand the
methods used to investigate them.

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